Contacts of the helix formed by residues 1186 - 1198 (chain 3) in PDB entry 6AH0
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU1186 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11843 SER 3.6 1.0 + - - -
11853 MET* 1.3 73.1 - - - +
11873 PRO* 1.3 67.1 - - - +
11883 ASN 3.2 2.9 - - - +
11893 LYS* 2.8 8.7 + - - +
11903 GLN 2.8 18.4 + - - -
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Residues in contact with PRO1187 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11853 MET 3.6 2.9 - - - +
11863 GLU* 1.3 70.5 - - - +
11883 ASN* 1.3 62.6 + - - +
11903 GLN* 2.9 3.6 + - - +
11913 LYS* 2.8 23.7 + - - -
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Residues in contact with ASN1188 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11863 GLU 3.2 1.2 - - - -
11873 PRO* 1.3 74.3 - - - +
11893 LYS* 1.3 57.7 + - - +
11913 LYS* 5.3 0.4 - - - +
11923 ASN* 2.9 28.3 + - - +
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Residues in contact with LYS1189 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11853 MET* 5.6 1.6 - - - +
11863 GLU* 2.8 11.3 + - - +
11883 ASN* 1.3 74.1 - - - +
11903 GLN* 1.3 66.2 + - - +
11933 VAL* 3.0 24.7 + - - +
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Residues in contact with GLN1190 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11823 PHE 5.1 10.8 - - - -
11853 MET* 5.0 3.6 - - - +
11863 GLU 2.8 15.9 + - - -
11873 PRO* 2.9 4.9 + - - -
11893 LYS* 1.3 74.1 - - - +
11913 LYS* 1.3 56.4 + - - +
11933 VAL* 4.1 0.2 - - - -
11943 SER* 3.0 20.1 + - - -
12013 PRO* 5.4 9.0 - - - +
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Residues in contact with LYS1191 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11873 PRO 2.8 13.2 + - - -
11883 ASN 4.8 0.2 - - - -
11893 LYS 3.0 0.2 + - - -
11903 GLN* 1.3 71.7 - - - +
11923 ASN* 1.3 56.3 + - - +
11933 VAL 3.0 2.2 - - - -
11943 SER* 2.3 30.6 + - - +
11953 GLU* 2.8 9.1 + - - -
12013 PRO 5.7 5.4 - - - -
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Residues in contact with ASN1192 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11883 ASN 2.9 21.5 + - - -
11913 LYS* 1.3 68.3 - - - +
11933 VAL* 1.3 61.2 + - - +
11953 GLU* 3.4 3.2 + - - +
11963 GLU* 3.0 17.5 + - - -
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Residues in contact with VAL1193 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11893 LYS* 3.0 14.9 + - - +
11903 GLN 4.1 0.4 - - - -
11913 LYS 2.7 3.0 + - - -
11923 ASN* 1.3 69.9 - - - +
11943 SER* 1.3 51.8 + - - +
11953 GLU 3.0 1.8 - - - -
11963 GLU* 2.5 25.3 + - - +
11973 LEU* 2.6 17.7 + - - -
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Residues in contact with SER1194 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11903 GLN 3.0 13.3 + - - -
11913 LYS* 2.3 17.7 + - - +
11933 VAL* 1.3 68.9 - - - +
11953 GLU* 1.3 47.4 + - - +
11973 LEU* 3.3 3.9 - - - +
11983 ASP 2.6 11.6 + - - -
11993 ARG* 2.4 47.4 + - - +
12003 THR 5.4 4.7 - - - -
12013 PRO* 6.2 0.2 - - - -
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Residues in contact with GLU1195 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11913 LYS 2.8 9.8 + - - -
11923 ASN* 3.7 4.5 - - - +
11933 VAL 2.8 0.4 + - - -
11943 SER* 1.3 72.7 - - - +
11963 GLU* 1.3 59.3 + - - +
11983 ASP* 2.4 29.0 + - - +
11993 ARG 3.8 4.1 + - - -
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Residues in contact with GLU1196 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11923 ASN 3.0 10.4 + - - -
11933 VAL* 2.5 13.1 + - - +
11953 GLU* 1.3 73.0 - - - +
11973 LEU* 1.3 59.3 + - - +
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Residues in contact with LEU1197 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11933 VAL 2.6 15.3 + - - -
11943 SER* 3.3 6.3 - - - +
11963 GLU* 1.3 71.8 - - - +
11983 ASP* 1.3 64.6 + - - +
11993 ARG 4.5 0.2 - - - +
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Residues in contact with ASP1198 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11943 SER 2.6 5.2 + - - -
11953 GLU* 2.4 29.3 + - - +
11963 GLU 3.0 0.6 + - - -
11973 LEU* 1.3 71.2 - - - +
11993 ARG* 1.3 55.7 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il